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| Status |
Public on Nov 09, 2023 |
| Title |
CAL148_RNA |
| Sample type |
SRA |
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| Source name |
breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: CAL148
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| Treatment protocol |
na
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| Growth protocol |
Cells were grown in their respective media prepared per provider's guidelines, at 37 degree C, 5% CO2.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Mini Kit.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw RNA-seq reads were aligned to version hg19 of the human genome and gene count and FPKM values were obtained using the VIPER pipeline {Cornwell, 2018, PMID: 29649993}, with parameters (stranded: true, library_type: ‘fr-firststrand’, filter_mirna: true).
Assembly: hg19
Supplementary files format and content: counts table and FPKM table
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| Submission date |
May 11, 2022 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
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| Phone |
617-632-2106
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| Organization name |
Dana-Farber Cancer Institute
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| Department |
Medical Oncology
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| Lab |
Polyak
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| Street address |
450 Brookline Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE202770 |
Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (TNBC cell lines RNA-Seq) |
| GSE202776 |
Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer |
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| Relations |
| BioSample |
SAMN28194321 |
| SRA |
SRX15235692 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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